Yes / Background: Soft tissue sarcomas are heterogeneous and a major complication in their management is that the existing classification scheme is not definitive and is still evolving. Leiomyosarcomas, a major histologic category of soft tissue sarcomas, are malignant tumours displaying smooth muscle differentiation. Although defined as a single group, they exhibit a wide range of clinical behaviour. We aimed to carry out molecular classification to identify new molecular subgroups with clinical relevance. Methods: We used gene expression profiling on 20 extra-uterine leiomyosarcomas and cross-study analyses for molecular classification of leiomyosarcomas. Clinical significance of the subgroupings was investigated. Results: We have identified two distinct molecular subgroups of leiomyosarcomas. One group was characterised by high expression of 26 genes that included many genes from the sub-classification gene cluster proposed by Nielsen et al. These sub-classification genes include genes that have importance structurally, as well as in cell signalling. Notably, we found a statistically significant association of the subgroupings with tumour grade. Further refinement led to a group of 15 genes that could recapitulate the tumour subgroupings in our data set and in a second independent sarcoma set. Remarkably, cross-study analyses suggested that these molecular subgroups could be found in four independent data sets, providing strong support for their existence. Conclusions: Our study strongly supported the existence of distinct leiomyosarcoma molecular subgroups, which have clinical association with tumour grade. Our findings will aid in advancing the classification of leiomyosarcomas and lead to more individualised and better management of the disease. / Alexander Boag Sarcoma Fund.

Introdução: Os ependimomas são tumores gliais raros e compreendem o terceiro tumor do sistema nervoso central mais frequente na infância. Apesar dos avanços terapêuticos, cerca de 50% dos pacientes desenvolvem recidiva local e 40% dos pacientes vão ao óbito. Uma das causas do insucesso das terapias é a alta heterogeneidade do tumor e a inconsistência do diagnóstico histológico. Em 2015, foi publicada pela primeira vez a caracterização molecular de ependimomas, sendo descrito nove subgrupos tumorais com perfis clínicos, demográficos e moleculares distintos. Objetivo: Estabelecer e padronizar a classificação molecular em amostras de ependimomas pediátricos e correlacionar a classificação com dados clínicos dos pacientes. Casuística e Métodos: Foram estudados 65 casos de ependimomas, diagnosticados no período entre 2001 a 2016 e provenientes do Hospital das Clínicas da Faculdade de Medicina de Ribeirão Preto e de São Paulo e do Centro Infantil Boldrini-Campinas. Vinte e seis casos eram ependimomas supratentoriais, classificados com base na presença de fusões gênicas C11orf95-RELA, YAP1-MAMLD1 e YAP1-FAM118B utilizando RT-PCR seguida por sequenciamento de Sanger. Trinta e nove casos de fossa posterior foram classificados em Grupos A, B ou não A e B através do perfil de expressão proteica e gênica dos marcadores: LAMA2, NELL2 e TNC utilizando imuno-histoquímica e PCR quantitativo em tempo real, respectivamente. Resultados: Dentre os ependimomas supratentoriais foram identificadas três amostras primárias e cinco amostras recidivadas com presença de fusão RELA, média de idade de 7 anos (variação de 2,6-13,7 anos), predominância do sexo masculino e grau de ressecção cirúrgica completa. Já a fusão YAP1- MAMLD1 foi identificada em quatro casos, diagnosticados em crianças mais novas, média de idade de 0,9 anos (variação de 0,75-2 anos). Adicionalmente, foi encontrado um caso variante em ependimoma supratentorial, denominado fusão C11orf95-LOC-RELA. Dentre os casos de ependimoma de fossa posterior, foram identificadas 26 amostras primárias e sete recidivas sugestivas de pertencerem ao Grupo A (LAMA2+/ NELL2 -) e seis amostras do Grupo não-A e não-B (LAMA2 +/ NELL2 + e LAMA2 -/NELL2-). Entre os pacientes considerados Grupo A, 90% (24/28) apresentaram marcação positiva para TNC, indicando serem tumores de pior prognóstico. A expressão gênica de LAMA2 e NELL2 apresentou correlação negativa e os genes TNC e LAMA2 uma correlação positiva, p<0,01 e p<0,05, respectivamente. Em ependimoma de fossa posterior Grupo A, os pacientes submetidos às ressecções completa e incompleta apresentaram diferença significativa na sobrevida global (5 anos) de 71,2% ± 14,5% versus 21,4% ± 17,8%, p< 0,01 e na SLE (2 anos) 63,5% ± 14,8% versus 25% ± 15.3%, p <0.001. Conclusões: De acordo com os resultados obtidos foi possível estabelecer a classificação molecular em uma casuística brasileira, seguindo os padrões descritos na literatura. Dados gerados a partir dessa padronização serão de fundamental importância para melhoria da estratificação tumoral, contribuindo tanto para determinação de estratégicas terapêuticas subgrupo-específicas, quanto na busca de novos alvos terapêuticos. / Introduction: Ependymomas are rare glial cell-derived tumors and comprise the third most frequent central nervous system tumor in childhood. Despite the therapeutic advances, about 50% of patients develop local recurrence and 40% of patients go to death. One of the causes of the failure of the therapies is the high tumor heterogeneity and the inconsistency of the histological diagnosis. In 2015, the molecular characterization of ependymomas was published for the first time, and nine tumor subgroups with distinct clinical, demographic and molecular profiles were described. Aim: To establish and standardize molecular classification in pediatric ependymoma samples and to correlate the classification with clinical data of the patients. Methods: We studied 65 cases of ependymomas, diagnosed between 2001 and 2016, from the Clinics Hospital of the Medical School of Ribeirão Preto and São Paulo and the Boldrini Children\'s Center-Campinas. Twenty-six cases were supratentorial ependymomas, classified based on the presence of gene fusions C11orf95- RELA, YAP1-MAMLD1 and YAP1-FAM118B using RT-PCR followed by Sanger sequencing. Thirty-nine posterior fossa cases were classified into Groups A, B or non A and B through the protein and gene expression profile of the markers: LAMA2, NELL2 and TNC using immunohistochemistry and quantitative real-time PCR, respectively. Results: Among the supratentorial ependymomas, three primary samples and five relapsed samples with RELA fusion, mean age of 7 years (range of 2.6-13.7 years), male predominance, and degree of complete surgical resection were identified. The YAP1-MAMLD1 fusion was identified in four cases, diagnosed in younger children, mean age 0.9 years (range of 0.75-2 years). In addition, a variant case was found in supratentorial ependymoma, called fusion C11orf95- LOC-RELA. Twenty-six primary samples and seven recurrences suggestive of Group A (LAMA2 + / NELL2-) and six non-A and non-B Group samples (LAMA2 + / NELL2 + and LAMA2 - / NELL2-). Among the patients considered Group A, 90% (24/28) presented positive staining for TNC, indicating that tumors had a worse prognosis. The gene expression of LAMA2 and NELL2 presented negative correlation and the TNC and LAMA2 genes had a positive correlation, p <0.01 and p <0.05, respectively. In the group A posterior fossa ependymoma, patients submitted to complete and incomplete surgical presented a significant difference in overall survival (5 years) of 71.2% ± 14.5% versus 21.4% ± 17.8%, p <0 , 01 and in SLE (2 years) 63.5% ± 14.8% versus 25% ± 15.3%, p <0.001. Conclusions: According to the results obtained, it was possible to establish the molecular classification in a Brazilian cohort, following the standards described in the literature. Data generated from this standardization will be of fundamental importance for the improvement of tumor stratification, contributing both to the determination of subgroup-specific therapeutic strategies and to the search for new therapeutic targets.

Submitted by Rafael Bispo Paschoalini (rbpaschoalini@gmail.com) on 2016-03-08T04:00:33Z No. of bitstreams: 1 Dissertação de mestrado - Rafael Bispo Paschoalini.pdf: 2764983 bytes, checksum: 576265167e590acb2641a540cda6283a (MD5) / Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-03-09T16:26:52Z (GMT) No. of bitstreams: 1 paschoalini_rb_me_bot.pdf: 2764983 bytes, checksum: 576265167e590acb2641a540cda6283a (MD5) / Made available in DSpace on 2016-03-09T16:26:52Z (GMT). No. of bitstreams: 1 paschoalini_rb_me_bot.pdf: 2764983 bytes, checksum: 576265167e590acb2641a540cda6283a (MD5) Previous issue date: 2016-02-26 / O carcinoma de mama é uma doença heterogênea. Pode ser classificado em fenótipos, com diferentes prognósticos, com base na expressão de determinadas proteínas. O fenótipo luminal é o mais frequente, correspondendo a cerca de 70% dos casos, sendo que tratamentos específicos para este fenótipo de carcinoma de mama já estão em estudo, com melhora promissora do prognóstico das pacientes acometidas. Entretanto, ainda não foram definidos critérios citológicos que pudessem predizer este fenótipo no material obtido pela punção aspirativa por agulha fina (PAAF). OBJETIVO: Investigar critérios citológicos individuais presentes na PAAF que possam se associar com o diagnóstico do fenótipo luminal do carcinoma de mama. MÉTODOS: Trata-se de estudo tipo corte-transversal, com componente descritivo e comparativo. As lâminas de PAAF e espécimes de carcinomas de mama invasivos ductais e lobulares, do período de 2000 a 2005, foram selecionados do arquivo do Laboratório de Patologia do Hospital Amaral Carvalho de Jaú/São Paulo, totalizando 297 casos. Dos blocos doadores foram extraídos cilindros de 2mm de diâmetro e depositados nos blocos de parafina receptores, usando Tissue Microarrays (Bencher Instruments®, Silver Spring, Maryland). Nestes cortes, foi feita a pesquisa imunoistoquímica para diferenciação dos fenótipos do carcinoma de mama, segundo a Classificação Molecular. As lâminas obtidas por PAAF, foram revisadas em microscópio de multiobservação (BX50 Olympus®, Japan), por dois médicos patologistas (RMD e FMN), sendo estudados individualmente os cinco critérios citológicos: celularidade, coesão celular, necrose, nucléolo e atipia nuclear. Utilizou-se o teste exato de Fisher para testar a associação entre os critérios citológicos e os fenótipos do carcinoma de mama. RESULTADOS: Dos 297 casos selecionados, 169 foram incluídos, resultando nos seguintes fenótipos - luminal A: 107 (63.3%), luminal B: 39 (23.1%), superexpressão de HER2: 8 (4.7%), e triplo negativo: 15 (8.9%). Os critérios citológicos que se associaram ao fenótipo luminal foram: celularidade baixa ou moderada (40.4%) (OR = 7.12, IC95%: 1.61 - 31.52), nucléolo inconspícuo ou presente (55.5%) (OR = 8.31, IC95%: 2.36 - 29.19) e atipia nuclear discreta ou moderada (44.5%) (OR = 8.42, IC95%: 1.90 - 37.25). Os critérios citológicos associados ao fenótipo luminal A foram: nucléolo inconspícuo ou presente (62.6%) (OR = 2.99, IC95%: 1.39 – 6.41), menor perda de coesão celular (OR = 0.46, IC95%: 0.24 - 0.88), mostrando grupamentos com coesão celular moderada a intensa, e ausência de necrose (40.2%) (OR = 0.32, IC95%: 0.15 – 0.68). CONCLUSÃO: Os critérios citológicos presentes nas lâminas obtidas por PAAF, e que mais se associaram ao fenótipo luminal do carcinoma de mama foram celularidade baixa e moderada, nucléolos inconspícuos ou pequenos e atipia nuclear leve a moderada. Cabe destacar, que para o fenótipo luminal A, os critérios citológicos que mais se associaram foram: nucléolos inconspícuos ou pequenos, coesão celular moderada a intensa e ausência de necrose. A distinção do fenótipo luminal é de relevância clínica, por apresentar melhor prognóstico, relacionado a menor mortalidade e menores taxas de metástase. / Breast carcinoma is a heterogeneous disease. It can be classified into phenotypes based on the expression of certain proteins, with differences in prognosis. The luminal phenotype is the most common, accounting for about 70% of cases. Some specific treatments for this phenotype of breast carcinoma are already being studied, which could improve prognosis of affected patients. However, there is currently no consensus on which cytological criteria could predict the luminal phenotype. OBJECTIVE: To evaluate which cytological criteria in fine-needle aspiration (FNA) biopsy are related with the luminal phenotype of breast carcinoma. METHODS: This was a cross-sectional study with descriptive and comparative component from cases of breast carcinomas, from the Laboratory of Pathology, Hospital Amaral Carvalho de Jaú / São Paulo. FNA biopsy specimens and tissue sections (mastectomy specimens) of invasive ductal and lobular carcinomas of the breast, retrieved from 2000 to 2005, were selected and classified into phenotypes by immunohistochemistry, using tissue microarray technology (Bencher Instruments®, Silver Spring, Maryland): luminal A and B, HER2 overexpression and triple negative. The cytological criteria for all cases were reviewed blindly by two pathologists using a multiobserver microscope (BX50 Olympus®, Japan), according to five cytological criteria: cellularity, cell cohesion, necrosis, nucleoli and nuclear atypia. Exact Fisher test was used to test the association between cytological criteria and phenotypes of breast carcinoma. RESULTS: From 297 selected patients, 169 were included, resulting in the following phenotypes - luminal A: 107 (63.3%), luminal B: 39 (23.1%), HER2 overexpression: 8 (4.7%), and triple negative: 15 (8.9%). The luminal phenotype showed mild or moderate cellularity (40.4%) (OR = 7.12, 95% CI: 1.61 - 31.52), inconspicuous or present nucleoli (55.5%) (OR = 8.31, 95% CI: 2.36 - 29.19) and mild or moderate nuclear atypia (44.5%) (OR = 8.42, 95% CI: 1.90 - 37.25). Inconspicuous or present nucleoli (62.6%) (OR = 2.99, 95% CI: 1.39 - 6.41), less dishesive cells (OR = 0.46, 95% CI: 0.24 - 0.88), showing clusters with moderate to intense cell cohesion (54.2%), and absence of necrosis (40.2%) (OR = 0.32, 95% CI: 0.15 - 0.68) were associated with luminal A phenotype. CONCLUSION: The individual FNA cytological criteria that might indicate the luminal phenotype of breast cancer were mild to moderate cellularity, inconspicuous or little nucleoli and mild to moderate nuclear atypia. Inconspicuous or little nucleoli, moderate to intense cell cohesion and absence of necrosis were associated with luminal A phenotype. The distinction of luminal phenotype of breast carcinoma is clinically relevant, since it has better prognosis, related to lower mortality and lower metastases rate.

Orientador: Rozany Mucha Dufloth / Resumo: O carcinoma de mama é uma doença heterogênea. Pode ser classificado em fenótipos, com diferentes prognósticos, com base na expressão de determinadas proteínas. O fenótipo luminal é o mais frequente, correspondendo a cerca de 70% dos casos, sendo que tratamentos específicos para este fenótipo de carcinoma de mama já estão em estudo, com melhora promissora do prognóstico das pacientes acometidas. Entretanto, ainda não foram definidos critérios citológicos que pudessem predizer este fenótipo no material obtido pela punção aspirativa por agulha fina (PAAF). OBJETIVO: Investigar critérios citológicos individuais presentes na PAAF que possam se associar com o diagnóstico do fenótipo luminal do carcinoma de mama. MÉTODOS: Trata-se de estudo tipo corte-transversal, com componente descritivo e comparativo. As lâminas de PAAF e espécimes de carcinomas de mama invasivos ductais e lobulares, do período de 2000 a 2005, foram selecionados do arquivo do Laboratório de Patologia do Hospital Amaral Carvalho de Jaú/São Paulo, totalizando 297 casos. Dos blocos doadores foram extraídos cilindros de 2mm de diâmetro e depositados nos blocos de parafina receptores, usando Tissue Microarrays (Bencher Instruments®, Silver Spring, Maryland). Nestes cortes, foi feita a pesquisa imunoistoquímica para diferenciação dos fenótipos do carcinoma de mama, segundo a Classificação Molecular. As lâminas obtidas por PAAF, foram revisadas em microscópio de multiobservação (BX50 Olympus®, Japan), por dois médicos p... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Breast carcinoma is a heterogeneous disease. It can be classified into phenotypes based on the expression of certain proteins, with differences in prognosis. The luminal phenotype is the most common, accounting for about 70% of cases. Some specific treatments for this phenotype of breast carcinoma are already being studied, which could improve prognosis of affected patients. However, there is currently no consensus on which cytological criteria could predict the luminal phenotype. OBJECTIVE: To evaluate which cytological criteria in fine-needle aspiration (FNA) biopsy are related with the luminal phenotype of breast carcinoma. METHODS: This was a cross-sectional study with descriptive and comparative component from cases of breast carcinomas, from the Laboratory of Pathology, Hospital Amaral Carvalho de Jaú / São Paulo. FNA biopsy specimens and tissue sections (mastectomy specimens) of invasive ductal and lobular carcinomas of the breast, retrieved from 2000 to 2005, were selected and classified into phenotypes by immunohistochemistry, using tissue microarray technology (Bencher Instruments®, Silver Spring, Maryland): luminal A and B, HER2 overexpression and triple negative. The cytological criteria for all cases were reviewed blindly by two pathologists using a multiobserver microscope (BX50 Olympus®, Japan), according to five cytological criteria: cellularity, cell cohesion, necrosis, nucleoli and nuclear atypia. Exact Fisher test was used to test the association between cy... (Complete abstract click electronic access below) / Mestre

Glioma, the tumor of glial cells, is one of the common types of primary central nervous system (CNS) neoplasms. Astrocytoma is the most common of all gliomas and originates from astrocytic glial cells. Astrocytoma tumors belong to two main categories: benign tumors, comprising of grade I Pilocytic astrocytoma and malignant tumors which diffusely infiltrate throughout the brain parenchyma. Diffusely infiltrating astrocytomas are graded into diffuse astrocytoma (DA; grade II), anaplastic astrocytoma (AA; grade III) and glioblastoma (GBM; grade IV) in the order of increasing malignancy. Patients with grade II astrocytoma have a median survival time of 6 to 8 years after surgical intervention. While the more aggressive grade III (AA) and grade IV (GBM) are together called malignant astrocytomas, the treatment protocols and length of survival are distinctly different between these grades. The median survival time for grade III patients is 2 to 3 years whereas patients with grade IV have a median survival of 12-15 months. GBMs have been further divided into primary GBM and secondary GBM on the basis of clinical and histopathological criteria. Primary GBM presents in an acute de novo manner with no evidence of an antecedent lower grade tumor and it accounts for >90% of all GBMs. In contrast, secondary GBM results from the progressive malignant transformation of a grade II or grade III astrocytoma. The current WHO grading system of astrocytomas is based on the histopathological characteristics of the underlying tumor tissue. Diagnoses by pathologists are dependent on specific histologic features: increased mitosis, nuclear atypia, microvascular proliferation and/or necrosis, which associate with biologically aggressive behaviour (WHO 2007). Though grading based on histology is largely reproducible and well accepted, subjectivity involved and substantial disagreement between pathologists has remained a major concern. Because of inherent sampling problems (mainly due to tumor location in the brain) and inadequate sample size available for histological evaluation, there exists a very high possibility of error in grading. Recent studies have attempted to characterize the molecular basis for the histological and prognostic differences between grade III and grade IV astrocytoma. While reports have shown the grade specific profile of gene expression, there is no molecular signature that can accurately classify grade III and grade IV astrocytoma samples. In the current work, we have identified molecular signatures for the accurate classification of grade III and grade IV astrocytoma patients by using transcriptome and miRNome data. The receptor tyrosine kinase pathway is known to be overexpressed in 88% of glioblastoma patients. The expression and activation of the receptors is reported to be deregulated by events like amplification and activating mutations. The aberrant expression of RTKs could also be due to the deregulation of miRNAs, which, in the untransformed astrocytes regulate and fine-tune the levels of the RTKs. In the current study, we have identified that tumor suppressor miRNA miR-219-5p regulates RTK pathway by targeting EGFR and PDGFRα. Part I. Transcriptome approach: Identification of a 16-gene signature for classification of malignant astrocytomas In order to obtain a more robust molecular classifier to accurately classify grade III and grade IV astrocytoma samples, we used transcriptome data from microarray study previously performed in our laboratory. The differential regulation of 175 genes identified from microarray was validated in a cohort of grade III and grade IV patients by real-time qRT-PCR. In order to identify the classification signature that can classify grade III and grade IV astrocytoma samples, we used the expression data of 175 genes for performing Prediction Analysis of Microarrays (PAM) in the training set of grade III and grade IV astrocytoma samples. PAM analysis identified the most discriminatory 16-gene expression signature for the classification of grade III and grade IV astrocytoma. The Principal Component Analysis (PCA) of 16-genes astrocytoma patient samples revealed that the expression of 16-genes could classify grade III and grade IV astrocytoma samples into two separate clusters. In the training set, the 16-gene signature was able to classify grade III and grade IV patients with an accuracy rate of 87.9% as tested by additional analysis of Cross-Validated probability by PAM. The 16-gene signature obtained in the training set was validated in the test set with diagnostic accuracy of 89%. We further validated the 16-gene signature in three independent cohorts of patient samples from publicly available databases: GSE1993, GSE4422 and TCGA datasets and the classification signature got validated with accuracy rates of 88%, 92% and 99% respectively. To address the discordance in grading between 16-gene signature and histopathology, we looked at the clinical features (age and survival) and molecular markers (CDKN2A loss, EGFR amplification and p53 mutation) that differ substantially between grade III and grade IV in discordant grade III and grade IV samples. The grading done by 16-gene signature correlated with known clinical and molecular markers that distinguish grade III and grade IV proving the utility of the 16-gene signature in the molecular classification of grade III and grade IV. In order to identify the pathways that 16 genes of the classification signature could regulate, we performed protein-protein interaction network and subsequently pathway analysis. The pathways with highest significance were ECM (extracellular matrix) and focal adhesion pathways, which are known to be involved in the epithelial to mesenchymal transition (EMT), correlating well with the aggressive infiltration of grade IV tumors. In addition to accurately classifying the grade III and grade IV samples, the 16-gene signature also demonstrated that genes involved in epithelial-mesenchymal transition play key role in distinguishing grade III and grade IV astrocytoma samples. Part II. miRNome approach microRNAs (miRNAs) have emerged as one of the important regulators of the interaction network that controls various cellular processes. miRNAs are short non-coding RNAs (mature RNA being 21-22nt long) that regulate the target mRNA by binding mostly in the 3’ UTR bringing about either translational repression or degradation of the target. miRNAs are shown to play key roles in cell survival, proliferation, apoptosis, migration, invasion and various other characteristic features that get altered in human cancers. miRNAs are characterized to have oncogenic or tumor suppressor role and the aberrant expression of miRNAs is reported in multiple human cancer types. Part A. Genome-wide expression profiling identifies deregulated miRNAs in malignant astrocytoma With an aim to identify the role of miRNAs in the development of in malignant astrocytoma, we performed a large-scale, genome-wide microRNA (miRNA) (n=756) expression profiling of 26 grade IV astrocytoma, 13 grade III astrocytoma and 7 normal brain samples. Using Significance Analysis of Microarrays (SAM), we identified several differentially regulated miRNAs between control normal brain and malignant astrocytoma, grade III and grade IV astrocytoma, grade III astrocytoma and grade IV secondary GBM, progressive pathway and de novo pathway of GBM development and also between primary and secondary GBM. Importantly, we identified a most discriminatory 23-miRNA expression signature, by using PAM, which precisely distinguished grade III from grade IV astrocytoma samples with an accuracy of 90%. We re-evaluated the grading of discordant samples by histopathology and identified that one of the discordant grade III samples had areas of necrosis and it was reclassified as grade IV GBM. Similarly, out of two discordant grade IV samples, one sample had oligo component and it was reclassified as grade III mixed oligoastrocytoma. Thus, after the revised grading, the prediction accuracy increased from 90% to 95%. The differential expression pattern of nine miRNAs was further validated by real-time RT-PCR in an independent set of malignant astrocytomas (n=72) and normal samples (n=7). Inhibition of two glioblastoma-upregulatedmiRNAs (miR-21 and miR-23a) and exogenous overexpression of two glioblastoma-downregulatedmiRNAs (miR-218 and miR-219-5p) resulted in reduced soft agar colony formation but showed varying effects on cell proliferation and chemosensitivity. Thus, we have identified the grade specific expression of miRNAs in malignant astrocytoma and identified a miRNA expression signature to classify grade III astrocytoma from grade IV glioblastoma. In addition, we have demonstrated the functional relevance of miRNA modulation and thus showed the miRNA involvement and their importance in astrocytoma development. Part B. miR-219-5p inhibits the receptor tyrosine kinase pathway by targeting mitogenic receptor kinases in glioblastoma The receptor tyrosine kinase (RTK) pathway, being one of the important growth promoting pathways, is known to be deregulated in 88% of the patients with glioblastoma. In order to understand the role of miRNAs in regulating the RTK pathway, we undertook a screening procedure to identify the potential miRNAs that could target different members of the RTK pathway. From the screening study involving bioinformatical prediction of miRNAs and subsequent experimental validation by modulation of miRNA levels in glioma cell lines, we identified miR-219-5p as a candidate miRNA. The overexpression of miR-219-5p reduced the protein levels of both EGFR and PDGFRα. We confirmed the binding of miR-219-5p to the 3’ UTRs by using reporter plasmids. We also confirmed the specificity of miR-219-5p binding sites in the 3’ UTR of EGFR by site directed mutagenesis of binding sites which abrogated the miRNA-UTR interaction. The expression of miR-219-5p was significantly downregulated in grade III as well as in grade IV astrocytoma samples in the miRNA microarray experiment and we further validated the downregulation in an independent cohort of grade III and grade IV astrocytoma patients by real-time qRT-PCR. The ectopic overexpression of miR-219-5p in glioma cell lines inhibited cell proliferation, colony formation, anchorage independent growth and the migration of glioma cells. In addition, overexpression of miR-219-5p decreased MAPK and PI3K pathways, in concordance with its ability to target EGFR and PDGFRα. Additionally, for the further characterization of miR-219-5p – EGFR interaction and its effect on MAPK and PI3K pathways, we used U87 glioma cells that stably overexpress wild-type EGFR and constitutively active ΔEGFR (both lacking 3’-UTR and thus being insensitive to miR-219-5p overexpression) along with U87 parental cells. In these cell lines with the overexpression of EGFR lacking 3’-UTR, miR-219-5p was unable to inhibit - MAPK and PI3K pathways and also glioma cell migration suggesting that these effects were indeed because of its ability to target EGFR. Further, in the glioblastoma patient cohort (TCGA dataset), we found significant negative correlation between EGFR protein levels, both total EGFR and phospho EGFR and miR-219-5p levels in the glioblastoma tissue samples suggesting a role of miR-219-5p in increasing the protein levels of EGFR in glioblastoma. In summary, we have identified and characterized miR-219-5p as the RTK regulating tumor suppressor miRNA in glioblastoma.

Le traitement systémique adjuvant du cancer du sein infiltrant repose sur la chimiothérapie et l’hormonothérapie. Certains facteurs sont connus pour être pronostiques (âge, taille tumorale, statut ganglionnaire, grade tumoral, emboles vasculaires, statut des récepteurs hormonaux (RH) et de HER2) ou prédictifs de réponse aux traitements (RH et HER2) et influent sur nos décisions thérapeutiques. Cependant, certaines patientes récidivent malgré un traitement complet alors que d’autres vont recevoir un traitement qui aurait pu être évité de par leur bon pronostic « intrinsèque ». Nous avons cherché à identifier dans ce travail d’autres facteurs pronostiques et / ou prédictifs dans le cancer du sein infiltrant en situation néoadjuvante / adjuvante. Premièrement, nous montrons que le type histologique lobulaire, réputé pour être une histologie de cancer du sein de bon pronostic et peu chimiosensible, ne doit pas être un facteur décisionnel quant aux traitements systémiques. En situation adjuvante et concernant la chimiothérapie, la validité et l’utilité cliniques des tests génomiques nécessitent d’être évaluées spécifiquement dans ce sous-groupe. Ensuite, nous avons étudié la validité analytique, la validité clinique et l’utilité clinique de 2 classifications moléculaires des cancers du sein selon PAM50 et l’analyse immunohistochimique de biomarqueurs : récepteur œstrogène, HER2 et Ki67 avec un cut-off à 14%. Selon nos conclusions, il n’y a actuellement pas de données suffisamment robustes pour que ces 2 classifications modifient les décisions de traitement systémique. Nous avons mis en évidence un sous-groupe de tumeurs triples négatives exprimant le récepteur androgène et FOXA1 et se comportant comme des tumeurs luminales. Enfin, nous avons montré sur une large série néoadjuvante que la réponse histologique complète est un critère substitutif de survie pour les tumeurs RH négatifs / The adjuvant systemic treatment of invasive breast cancer is based on chemotherapy and endocrine therapy. Several prognostic factors (age, tumoral size, nodal status, tumoral grade, vascular embols, hormonal receptors (HR), HER2) and predictive factors of response to treatment (HR and HER2) are described and have an impact on our therapeutic decisions. However, recurrences are frequent after a complete treatment and patients could avoid such treatment because of the good “intrinsic” prognosis. In this work, we aimed to identify other prognostic and / or predictive factors for the invasive breast cancer in the neoadjuvant / adjuvant settings. Firstly, we showed that the lobular histology, considered as histology of good prognosis and low chemo sensitive, should not be a decisive factor regarding systemic therapy. In the adjuvant setting, regarding chemotherapy, clinical validity and utility of the genomic tests need to be specifically evaluated in this subgroup. Then, we studied analytical validity, clinical validity and clinical utility of 2 molecular classification of breast cancer: PAM50 and a panel of 3 biomarkers in immunohistochemistry (estrogen receptor, HER2 and Ki-67 with a cut-off of 14%). We concluded that the data were not strong enough and that the therapeutic decisions should not be influenced by these classifications. We identified a subgroup of triple negative breast cancer that express androgen receptor and FOXA1 and which behave like luminal tumors. At last, we showed in a large neoadjuvant population, that the pathological complete response is a surrogate marker of survival in RH negative tumors

Les leucémies myéloïdes aiguës (LMA) consistent en un groupe de cancers agressifs causés par une accumulation de mutations génétiques et épigénétiques survenant dans les cellules souches ou progénitrices de la moelle osseuse. Il s’agit d’un groupe de maladies très hétérogène, caractérisé par un grand nombre de combinaisons d’altérations qui perturbent à la fois les voies de signalisation qui y sont exprimées, leur sensibilité aux différents traitements et le pronostic des patients. Le déploiement des technologies de séquençage de nouvelle génération au courant de la dernière décennie a permis l’exploration à une échelle sans précédent du paysage mutationnel et transcriptomique de différents cancers, incluant les LMA. Dans le cadre de nos travaux, nous avons voulu tester l'hypothèse selon laquelle les LMA se déclinent en plusieurs sous-groupes génétiques caractérisés chacun par des mutations distinctes et une expression génique dérégulée, ainsi qu’une réponse différentielle à des molécules qui pourraient représenter de nouvelles stratégies thérapeutiques. Nous avons testé cette hypothèse au sein de la cohorte Leucegene, qui comprend un grand nombre de LMA primaires analysées par le séquençage du transcriptome, et nous avons analysé les différences entre les différents sous-groupes en les analysant un à la fois. Cette étude des différents sous-groupes nous a permis de disséquer le profil génomique, transcriptomique et les sensibilités aux petites molécules de sept sous-groupes génétiques, représentant environ la moitié des cas de LMA de l’adulte. Notre approche a permis de découvrir plusieurs nouvelles mutations spécifiques aux différents sous-groupes, dont certaines ont été validées dans des cohortes indépendantes. Nous avons également confirmé que les gènes différentiellement exprimés dans les sous-groupes sont plus informatifs que les signatures d'expression non supervisées pour identifier les biomarqueurs de la maladie. Nous avons ainsi identifié dans la majorité des sous-groupes des gènes représentant un biomarqueur d'intérêt, ayant une pertinence fonctionnelle ou pronostique. Ces données ont également mené à des criblages chimiques ciblés qui ont identifié de nouvelles vulnérabilités dépendant du contexte génétique. Au-delà de ces observations, nos travaux pourraient avoir une portée translationnelle tandis que le séquençage de nouvelle génération est de plus en plus utilisé en clinique. La combinaison avec d’autres modalités de séquençage et l’incorporation de technologies émergentes aideront à poursuivre la dissection génomique, transcriptomique et chimique de la LMA et l’approche utilisée pourra même éventuellement s’appliquer à d’autres types de cancers. / Acute myeloid leukemias (AML) are a group of cancers caused by an accumulation of genetic and epigenetic mutations occurring in the stem or progenitor cells of the bone marrow. They represent a very heterogeneous group of diseases, characterized by a large number of combinations of alterations which disrupt to varying degrees key networks in these cells, their sensitivity to treatments and the prognosis of the patients. The deployment of next-generation sequencing technologies over the past decade has enabled exploration on an unprecedented scale of the mutational and transcriptomic landscape of various cancers, including AML. As part of our work, we tested the hypothesis according to which AMLs comprise several genetic subgroups, each characterized by distinct mutations and deregulated gene expression profiles, as well as a differential response to molecules that could represent novel therapies. We tested this hypothesis in the Leucegene cohort, which includes a large number of primary AMLs analyzed by transcriptome sequencing, which we explored one subgroup after the other, dissecting the genomic, transcriptomic or small molecule sensitivities profile of seven AML subgroups representing approximately half of adult AML cases. Our approach has allowed us to discover several new mutations specific to different subgroups, some of which have been validated in independent cohorts. We also confirmed that genes differentially expressed in subgroups are more informative than unsupervised expression signatures, and we identified genes representing potential biomarkers, or having a functional or prognostic relevance in the majority of subgroups. Generated data also led to targeted chemical screens performed on primary AML cells, which identified new context-dependent vulnerabilities. Beyond these observations, our work could have a translational scope while next-generation sequencing is paving its way in the clinic. The combination with other Omics and the incorporation of emerging technologies will help to further the multi-dimensional dissection of these groups and additional ones, as the presented approach could be applied to additional disease subsets and cancer types.